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optitype  (CeGAT GmbH)

 
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    CeGAT GmbH optitype
    Optitype, supplied by CeGAT GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/optitype/optitype/pm33689574-48-54-55
    Average 90 stars, based on 1 article reviews
    optitype - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    RNA Sequencing:

    Article Title: Neoantigen-reactive T cells exhibit effective anti-tumor activity against colorectal cancer.
    Article Snippet: .. For RNA-seq, RNA reads were compared with the hg19 reference genome and transcriptome using Bowtie.16 We determined gene expression by comparing known gene transcripts with detailed exon coordinates in UCSC and then normalized to the RPKM units.17 Human leukocyte antigen typing The HLA alleles of each patient were identified from the WES data using OptiType (CeGaT GmbH, Tubingen, Germany)18 with the default settings after filtering the reads aligning to the HLA region using RazerS version 3.4.0 (GitHub Inc., San Francisco, USA).19 ..

    Gene Expression:

    Article Title: Neoantigen-reactive T cells exhibit effective anti-tumor activity against colorectal cancer.
    Article Snippet: .. For RNA-seq, RNA reads were compared with the hg19 reference genome and transcriptome using Bowtie.16 We determined gene expression by comparing known gene transcripts with detailed exon coordinates in UCSC and then normalized to the RPKM units.17 Human leukocyte antigen typing The HLA alleles of each patient were identified from the WES data using OptiType (CeGaT GmbH, Tubingen, Germany)18 with the default settings after filtering the reads aligning to the HLA region using RazerS version 3.4.0 (GitHub Inc., San Francisco, USA).19 ..

    other:

    Article Title: Neoantigen-reactive T cells exhibit effective anti-tumor activity against colorectal cancer
    Article Snippet: The HLA alleles of each patient were identified from the WES data using OptiType (CeGaT GmbH, Tubingen, Germany) with the default settings after filtering the reads aligning to the HLA region using RazerS version 3.4.0 (GitHub Inc., San Francisco, USA).



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    (A) <t>HLA-B</t> allele alignment of next generation sequencing data for one sample in HLA Explore software (exons 1–4). This sample resulted in a failure or “no call” for the HLA-B locus; however, by actual HLA typing was found to be HLA-B*44:02:01/*56:01:01. The top row shows the correct alignment of reads (represented by stacked grey bars) to the HLA-B*56:01:01 allele from exon 1 (left side) to exon 4 (right side of diagram), while the middle row shows reads unevenly and incorrectly mapping to the HLA-B*83:01 allele, and the bottom row shows a lack of reads mapping to the correct HLA-B*44:02:01 allele. (B) In contrast, the <t>Optitype</t> plots for the same sample are shown. This software produced a call concordant to the second field for each allele.
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    Image Search Results


    (A) HLA-B allele alignment of next generation sequencing data for one sample in HLA Explore software (exons 1–4). This sample resulted in a failure or “no call” for the HLA-B locus; however, by actual HLA typing was found to be HLA-B*44:02:01/*56:01:01. The top row shows the correct alignment of reads (represented by stacked grey bars) to the HLA-B*56:01:01 allele from exon 1 (left side) to exon 4 (right side of diagram), while the middle row shows reads unevenly and incorrectly mapping to the HLA-B*83:01 allele, and the bottom row shows a lack of reads mapping to the correct HLA-B*44:02:01 allele. (B) In contrast, the Optitype plots for the same sample are shown. This software produced a call concordant to the second field for each allele.

    Journal: Human immunology

    Article Title: Concordance between predicted HLA type using next generation sequencing data generated for non-HLA purposes and clinical HLA type

    doi: 10.1016/j.humimm.2020.06.002

    Figure Lengend Snippet: (A) HLA-B allele alignment of next generation sequencing data for one sample in HLA Explore software (exons 1–4). This sample resulted in a failure or “no call” for the HLA-B locus; however, by actual HLA typing was found to be HLA-B*44:02:01/*56:01:01. The top row shows the correct alignment of reads (represented by stacked grey bars) to the HLA-B*56:01:01 allele from exon 1 (left side) to exon 4 (right side of diagram), while the middle row shows reads unevenly and incorrectly mapping to the HLA-B*83:01 allele, and the bottom row shows a lack of reads mapping to the correct HLA-B*44:02:01 allele. (B) In contrast, the Optitype plots for the same sample are shown. This software produced a call concordant to the second field for each allele.

    Article Snippet: A , Pre-NAC , Concordant , Omixon – No Call (both alleles); Optitype & HLA-Genotyper – Concordant , Concordant , Omixon - No Call (one allele); HLA-Genotyper - Concordant , Concordant , Omixon - No Call (one allele); HLA-Genotyper-Concordant.

    Techniques: Next-Generation Sequencing, Software, Produced

    Summary of concordance between actual HLA typing by SSO and predicted typing by next generation sequencing by locus. Number (percentage) of alleles (for 68 samples from Data Set 1: Germline Whole Exome Sequencing of Patients with Breast Cancer) is provided. A) Using Omixon software; B) Using OptiType software; C) Using HLA-Genotyper software. Full results are available in the Supplementary materials .

    Journal: Human immunology

    Article Title: Concordance between predicted HLA type using next generation sequencing data generated for non-HLA purposes and clinical HLA type

    doi: 10.1016/j.humimm.2020.06.002

    Figure Lengend Snippet: Summary of concordance between actual HLA typing by SSO and predicted typing by next generation sequencing by locus. Number (percentage) of alleles (for 68 samples from Data Set 1: Germline Whole Exome Sequencing of Patients with Breast Cancer) is provided. A) Using Omixon software; B) Using OptiType software; C) Using HLA-Genotyper software. Full results are available in the Supplementary materials .

    Article Snippet: A , Pre-NAC , Concordant , Omixon – No Call (both alleles); Optitype & HLA-Genotyper – Concordant , Concordant , Omixon - No Call (one allele); HLA-Genotyper - Concordant , Concordant , Omixon - No Call (one allele); HLA-Genotyper-Concordant.

    Techniques: Next-Generation Sequencing, Sequencing, Software

    Summary of concordance of HLA calls generated by actual HLA typing (SSO) and predicted typing by next generation sequencing by locus for tumor specimens of each of the 5 subjects. The tumor from subject A was typed at 4 different time points. Full data is available in the Supplementary materials .

    Journal: Human immunology

    Article Title: Concordance between predicted HLA type using next generation sequencing data generated for non-HLA purposes and clinical HLA type

    doi: 10.1016/j.humimm.2020.06.002

    Figure Lengend Snippet: Summary of concordance of HLA calls generated by actual HLA typing (SSO) and predicted typing by next generation sequencing by locus for tumor specimens of each of the 5 subjects. The tumor from subject A was typed at 4 different time points. Full data is available in the Supplementary materials .

    Article Snippet: A , Pre-NAC , Concordant , Omixon – No Call (both alleles); Optitype & HLA-Genotyper – Concordant , Concordant , Omixon - No Call (one allele); HLA-Genotyper - Concordant , Concordant , Omixon - No Call (one allele); HLA-Genotyper-Concordant.

    Techniques: Generated, Next-Generation Sequencing